Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 809c087a8a50e30c7606b7b09e8c989d2b3ed6c8 https://github.com/galaxyproject/galaxy/commit/809c087a8a50e30c7606b7b09e8c9... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-01-24 (Tue, 24 Jan 2017)
Changed paths: M lib/galaxy/webhooks/__init__.py A test/api/test_webhooks.py
Log Message: ----------- - add Webhooks tests - small code improvements
Commit: 867e8dc4ca9aa3055a0149de594bae8fab4f8d13 https://github.com/galaxyproject/galaxy/commit/867e8dc4ca9aa3055a0149de594ba... Author: John Chilton jmchilton@gmail.com Date: 2017-01-24 (Tue, 24 Jan 2017)
Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css
Log Message: ----------- Treat demo/test webhooks like demo/test tools.
- Populate test server with demo webhooks by default. - Eliminate special logic needed to treat the demo directory differently. - Document how to enable the demo webhooks in galaxy.ini.sample. - Populate the demo webhooks when starting Galaxy with GALAXY_RUN_WITH_TEST_TOOLS=1 set.
Commit: 8b30d874b539aa9665387bc298e1fbb528c242d0 https://github.com/galaxyproject/galaxy/commit/8b30d874b539aa9665387bc298e1f... Author: John Chilton jmchilton@gmail.com Date: 2017-01-24 (Tue, 24 Jan 2017)
Changed paths: M test/api/test_webhooks.py
Log Message: ----------- Update webhooks API test to set expectations independent of implementation.
It may seem like this is testing less since fewer API calls are being made - but when you use the backend to generate the data you trust in the test case - the correlation lands up meaning relatively less is tested. For instance, if there is some problem arises in the to_dict method of a webhook - it is going to arise in both the implementation and in the test case and so the test case will just be asserting that the response is broken ... and it will be. Testing more concrete things is also good for ensuring backward compatibility.
Commit: a9ba71c07be195f0e0b1774a802ed919d3a4f2b1 https://github.com/galaxyproject/galaxy/commit/a9ba71c07be195f0e0b1774a802ed... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-01-25 (Wed, 25 Jan 2017)
Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh M test/api/test_webhooks.py M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css
Log Message: ----------- Merge pull request #3 from jmchilton/webhooks_reorg
Improve abstraction in webhook API tests.
Commit: 41d4eac28ff14b334bf413e75e81401a458334e0 https://github.com/galaxyproject/galaxy/commit/41d4eac28ff14b334bf413e75e814... Author: John Chilton jmchilton@gmail.com Date: 2017-01-29 (Sun, 29 Jan 2017)
Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.history.yaml M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A display_applications/igv/genome_fasta.xml M doc/schema_template.md M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M doc/source/dev/faq.rst M doc/source/dev/interactive_environments.rst M lib/galaxy/auth/providers/__init__.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py A lib/galaxy/datatypes/converters/fasta_to_fai.xml A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.smat A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/shell/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/condor/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M 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lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy/workflow/steps.py M lib/galaxy_utils/sequence/sequence.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M run.sh M run_tests.sh M scripts/bootstrap_history.py M scripts/functional_tests.py A scripts/manage_tool_dependencies.py R scripts/run_selenium_tests.sh M static/maps/layout/menu.js.map A static/maps/libs/showdown.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/workflow/workflow-canvas.js.map A static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js A static/scripts/libs/showdown.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M templates/ind_share_base.mako M templates/show_params.mako M templates/webapps/galaxy/history/share.mako R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py A test/api/test_visualizations.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js M test/docker/README.md M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/tools/column_param.xml A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml A test/functional/tools/explicit_conversion.xml A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml A test/functional/tools/mulled_example_conflict.xml A test/functional/tools/paired_collection_map_over_structured_like.xml A test/functional/tools/param_text_option.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/phdcomics/static/script.js R test/functional/workflow.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/sizzle.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/tests/workflow_editor_tests.js A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py R tools/filters/gff/sort_gtf.py M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini
Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into feature/webhooks_tests
Commit: 4cb7617bb815b455edb5307759318822944f5a3c https://github.com/galaxyproject/galaxy/commit/4cb7617bb815b455edb5307759318... Author: John Chilton jmchilton@gmail.com Date: 2017-01-29 (Sun, 29 Jan 2017)
Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh A test/api/test_webhooks.py M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css
Log Message: ----------- Merge pull request #3469 from anatskiy/feature/webhooks_tests
Webhooks: add tests
Compare: https://github.com/galaxyproject/galaxy/compare/30b462190ac7...4cb7617bb815